The first time I fought Atris I left her to the Sith holocrons. Looking back on it, it is a pretty merciless thing to do (I was pure LS by that point) but it seemed a fitting end to her. I don't remember what I did the second time, but I've never killed her.
I left Vaklu's fate to Queen Talia, that was just how it should be.
I kill exchange members without a second thought most of the time.